getGeneSim: Compute functional similarity for genes

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/geneSimilarity.R

Description

Calculate the pairwise functional similarities for a list of genes using different strategies.

Usage

1
getGeneSim(genelist1, genelist2=NULL, similarity="funSimMax", similarityTerm="relevance", normalization=TRUE, method="sqrt", avg=(similarity=="OA"), verbose=FALSE)

Arguments

genelist1

character vector of primary gene IDs according to organism annotation package (see setEvidenceLevel)

genelist2

optional other character vector of primary gene IDs to compare against

similarity

method to calculate the functional similarity between gene products

similarityTerm

method to compute the similarity of GO terms

normalization

normalize similarities yes/no

method

"sqrt": normalize sim(x,y) <- sim(x,y)/sqrt(sim(x,x)*sim(y,y)); "Lin": normalize sim(x,y) <- 2*sim(x,y)/(sim(x,x) + sim(y,y)); "Tanimoto": normalize sim(x,y) <- sim(x,y)/(sim(x,x) + sim(y,y) - sim(x,y)). NOTE: normalization does not have any effect, if term similarity is NOT "relevance" and similarity = "funSimMax", "funSimAvg" or similarity = "OA" and avg=TRUE

avg

standardize the OA kernel by the maximum number of GO terms for both genes

verbose

print out some information

Details

The method to calculate the pairwise functional similarity between gene products can either be:

"max"

the maximum similarity between any two GO terms

"mean"

the average similarity between any two GO terms

funSimMax

the average of best matching GO term similarities. Take the maximum of the scores achieved by assignments of GO terms from gene 1 to gene 2 and vice versa. [2]

funSimAvg

the average of best matching GO term similarities. Take the average of the scores achieved by assignments of GO terms from gene 1 to gene 2 and vice versa. [2]

"OA"

the optimal assignment (maximally weighted bipartite matching) of GO terms associated to the gene having fewer annotation to the GO terms of the other gene. [1]

"hausdorff"

Hausdorff distance between two sets: Let X and Y be the two sets of GO terms associated to two genes. Then dist(X,Y) = \max\{\sup_{t \in X} \inf_{t' \in Y} d(t,t'), \sup_{t' \in Y} \inf_{t \in X} d(t,t') [3]. Since GOSim 1.2.8 we translate the Haussdorff distance into a similarity measure by taking sim(X,Y) = \exp(-dist(X,Y).

"dot"

the dot product between feature vectors describing the absence/presence of each GO term. The absence of each GO term is weighted by its information content. Depending on the type of later normalization one can arrive at the cosine similarity (method="sqrt") or at the Tanimoto coefficient (method="Tanimoto").[4]

Value

n x n similarity matrix (n = number of genes)

Note

The result depends on the currently set ontology.

Author(s)

Holger Froehlich

References

[1] H. Froehlich, N. Speer, C. Spieth, A. Zell, Kernel Based Functional Gene Grouping, Proc. Int. Joint Conf. on Neural Networks (IJCNN), 6886 - 6891, 2006.

[2] A. Schlicker, F. Domingues, J. Rahnenfuehrer, T. Lengauer, A new measure for functional similarity of gene products based on Gene Ontology, BMC Bioinformatics, 7, 302, 2006.

[3] A. del Pozo, F. Pazos, A. Valencia, Defining functional distances over Gene Ontology, BMC Bioinformatics, 9:50, 2008.

[4] M. Mistry, P Pavlidis, Gene Ontology term overlap as a measure of gene functional similarity, BMC Bioinformatics, 9:327, 2008.

See Also

getGeneSimPrototypes, getTermSim, setOntology

Examples

1
	# see evaluateClustering

Example output

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Loading required package: annotate
Loading required package: XML

GOSim documentation built on Nov. 1, 2018, 2:26 a.m.